Table of contents for Bioinformatics / edited by Paul H. Dear.


Bibliographic record and links to related information available from the Library of Congress catalog
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Chapter 1. Database resources for wet-bench scientists
Neil Hall and Lynn M. Schriml
1.  Introduction                                                  1
1.1 Types of databases                                         1
1.2  Database resources at NCBI                               2
2. Methods and approaches                                         4
2.1 Searching databases at NCBI                                4
2.2  Downloading NCBI datasets                                11
3. Troubleshooting                                               11
4. Additional web resources                                      12
5. References                                                    13
Chapter 2. Navigating sequenced genomes
Melody S. Clark and Thomas Schlitt
1.  Introduction                                                 15
2. Methods and approaches                                        16
2.1 Finding genome resources for an organism                  16
2.2  Browsing vertebrate genomes with Ensembl                 18
2.3 Integr8 - an Ensembl lookalike for microbes               22
2.4 Other web-based genome browsers                           24
2.5 Specialized sites                                         26
2.6 Downloading data with BioMart                             27
2.7 Browsing genomes 'off line' using stand-alone software    30
2.8 Linking your own data to a genome browser                 33
3. References                                                    38
Chapter 3. Sequence similarity searches
Jaap Heringo and Walter Pirovano
1. Introduction                                                   39
1.1 Comparative sequence analysis                              39
1.2 Sequence alignment as a reflection of similarity           39
1.3 Similarity versus homology                                 40
1.4 Techniques for pairwise alignment                          41
1.5 Alignment scores as a measure of similarity                42
1.6 Sequence identity as a measure of similarity               43
1.7 Statistics of alignment similarity scores                  43
1.8  Protein domains                                           44
2. Methods and approaches                                         44
2.1 Should one compare protein or nucleotide sequences?        45
2.2 Curated and annotated sequence databases                   46
2.3 Heuristic sequence similarity searching methods            47
2.4 Statistical significance of search results - E values      56
2.5 Fast Smith-Waterman local alignment searches               59
2.6 Profile searching                                          60
3. Troubleshooting                                                65
3.1 Iterative homology searching problems                      65
3.2 Post-processing of homology searches                       66
3.3 Evaluating sequence database searches                      66
4. References                                                     67
Chapter 4. Gene prediction
Marie-Adele Rajandream
1.  Introduction                                                  71
1.1 Ab initio methods                                          72
1.2 Comparative methods                                        73
2. Methods and approaches                                         74
2.1 Predicting eukaryotic genes                                75
2.2  Predicting prokaryotic genes                              90
3. Troubleshooting                                                98
4. Additional web resources                                       99
5. References                                                    101
Chapter 5. Prediction of noncoding transcripts
Alex Bateman and Sam Griffiths-Jones
1.  Introduction                                                 103
2. Methods and approaches                                        105
2.1 Ab initio versus family-specific searches                 105
2.2 Web servers for the detection of single, specific RNA classes  106
2.3 Web servers for the prediction of multiple RNA classes     111
3. Troubleshooting                                                114
3.1 RNA-derived repeats and pseudogenes                        114
3.2  Computational complexity                                  115
4. References                                                     115
Chapter 6. Finding regulatory elements in DNA sequence
Debraj GuhaThokurta ond Gory D. Stormo
1.  Introduction                                                  117
1.1 Background                                                 117
1.2 An overview of progress in the computational identification
of DNA sequence motifs                                    118
1.3  Modeling and representation of DNA motifs                 119
2. Methods and approaches                                         123
2.1 Searching DNA for known motifs                             123
2.2  Discovery of DNA motifs from input DNA sequences          126
2.3  Comparative genomics and phylogenetic footprinting in the
search for DNA regulatory elements                        132
2.4  Composite DNA motifs and cis-regulatory modules           134
3. Additional web resources                                       135
4. References                                                     136
Chapter 7. Expressed sequence tags
Arthur Gruber
1. Introduction                                                   141
1.1 EST library construction and sequencing                    142
1.2  Representation: normalized and subtracted libraries       144
2. Methods and approaches                                         145
2.1 Overview                                                   145
2.2 EST databases                                              146
2.3 Automated EST pre-processing pipelines                     150
2.4 Transcript reconstruction                                  155
2.5  Redundancy estimation                                     160
2.6  Electronic gene expression profiles                       162
2.7  Mapping ESTs to the genome                                162
3. Troubleshooting                                                163
3.1 Clone chimerism                                            163
3.2  SNPs                                                      164
3.3  Repeat masking                                            164
3.4  Contamination                                             164
4. Additional web resources                                       164
5. References                                                     165
Chapter 8. Protein structure, classification, and prediction
Arthur M. Lesk
1. Introduction                                                   169
1.1 The chemical structure of proteins                         170
1.2 The hierarchical form of protein architecture              172
1.3  Domains                                                   173
2. Methods and approaches                                         173
2.1 Accessing macromolecular structures on the web             173
2.2  Classification of protein structures                      176
2.3 Structural genomics                                        180
2.4 Approaches to protein structure prediction                 180
2.5 Specialized methods for particular types of structure      186
3. References                                                     194
Chapter 9. Gene ontology
Vineet Sangar
1. Introduction                                                   195
1.1 Gene ontology                                              196
1.2 Structure of the GO database                               196
1.3 The three GO ontologies                                    198
1.4  GO terms                                                  199
1.5 Evidence codes                                             199
2. Methods and approaches                                         200
2.1 GO browsers                                                200
2.2  GO annotation tools                                       204
2.3  Gene expression tools                                     205
2.4 Integration of GO with other classification systems        206
3. Additional web resources                                       206
4. References                                                     207
Chapter 10. Prediction of protein function
Rodrigo Lopez
1. Introduction                                                   209
2. Methods and approaches                                         210
2.1 Required tools                                             210
2.2  Prediction and determination of physicochemical
properties of proteins                                    210
2.3  Determination of secondary structure from sequence        215
2.4  Determination of functional domains using pattern-matching
methods                                                   224
2.5 Advanced methods combining several protein function
prediction algorithms                                     230
2.6  Protein function prediction by transfer of annotation     233
2.7  Multiple sequence alignments and secondary databases      234
2.8 An overview of InterPro and CDD                            235
2.9  Recent advances in protein function prediction            238
2.10 Concluding remarks                                        241
3. Additional web resources                                       241
4. References                                                     242
Chapter 11. Multiple sequence alignment
Burkhord Morgenstern
1.  Introduction
2. Methods and approaches                                      246
2.1 The alignment problem in computational biology          246
2.2 Pairwise sequence alignment                             247
2.3 Multiple sequence alignment                             249
2.4 Benchmarking and evaluation of multiple-alignment software  250
2.5 Visualization and comparison of multiple alignments     251
2.6 Multiple alignment of large genomic sequences           251
2.7 Software tools for multiple alignment                   252
3. Additional web resources
4. References                                                  262
263
Chapter 12. Inferring phylogenetic relationships from sequence data
Peter G. Foster
1. Introduction
2. Methods and approaches                                      265
2.1 Alignments                                              269
2.2 File formats                                            269
2.3 Software                                                269
2.4 Tree-building methods                                   270
2.5 Choosing a model                                        271
2.6 A Bayesian approach to phylogenetics                    274
3. Troubleshooting                                             278
4. References                                                  280
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Library of Congress subject headings for this publication: Bioinformatics